Showing posts with label Data. Show all posts
Showing posts with label Data. Show all posts

Thursday, February 21, 2013

4 Things I Wish I Knew Before Starting Grad School

February 21, 2013 0

Gastric bypass- a wonderful alternative to graduate school

'Tis the season of grad school acceptances and major life choices. Two years ago (!) I was an overly confident undergrad preparing to become a graduate researcher. Late night Googling of "how to prepare for grad school" further assured me I was ready. Have experience in a research lab? Check. Know I may have weird hours? Check. Secured some kind of TA/RA funding? Check. Today, reflecting upon this time of year, I wish someone would have told me about a few aspects of grad school that seem to never be highlighted on those "What to Know about Grad School" websites:


1. Yes, being successful in grad school is about working hard, but it’s even more about being creative.

Probably in your undergrad studies, the more time spent on homework or a project was directly proportional to your grades or success. I assumed that since I was a hard worker and previously worked in a research lab, I would be a great grad student. However, once you enter a graduate program, you are likely designing your own study and teaching yourself research methods. In other words, your success is entirely dependent on your creativity. If your plan is to research whales in the Antarctic, for example, you will have to figure out HOW you are getting to the Antarctic, HOW many whales you are tagging, HOW you are tagging the whales, and most importantly, HOW you are paying for it- not your advisor, not your department, not your best friend- YOU. Also, you will have to go way beyond the idea of “I want to study whales in the Antarctic.” You will have to come up with testable hypotheses, such as “Using complicated organic chemistry, I will show that the number of female whales in January positively correlates with annual apple harvests in United States- here’s how I will experimentally prove it…”

2. Often in the sciences there is not a specific timeline for graduation.

Many students entering grad school enter with the belief that getting a master’s degree will be completed in exactly 2 years while a PhD takes 4 years to complete. Most people are familiar with the undergrad concept of schooling: when you earn X number of credits, which should take Y years to complete, you get your degree. The timeline of your graduation, however, is ENTIRELY dependent on your thesis/dissertation progress. Have your class credits out of the way? GREAT! Experiments not working- well, you’re staying here another 3 years.

3. Be prepared for the fact that no one will respect your “flexible” schedule.

Because you likely aren’t confined to a 9-5 schedule, your friends with "real jobs" will assume you are always available to talk on the phone, pick them up from the airport, help them move, do their weekly grocery shopping, groom their monitor lizard, etc. Additionally, when they are free from work, they assume you are as well. “Hey, I got tickets to Soviet Russia the Musical without consulting you; you can write your thesis some other time.” The best way to deal with this is to simply lie: “I teach 9 classes and no one can replace me.”

4. Unless you clone yourself, someone will see you as a bad grad student.

Many times you will have an obligation to be in 3 or 4 places at once.  Tomorrow, for example, I have boat crew training, which is required for my field work.  This time spent on training, however, means I'm not working on my thesis writing, not working on homework, not available for makeup labs with my students, and not attending the weekly grad seminar.  Somewhere along this line, a student of mine, a professor in my department, one of my committee members, or my neglected dog will wonder where I am and why I am a horrible person.  And why did I spend so much time writing this blog post?

Tuesday, November 20, 2012

Helpful Websites - My Parting Gift to You

November 20, 2012 0
As I sit here struggling to write my very last blog post, I wonder "What can I leave people that they'll find useful in any way?"  I could provide meaningful insight on what it was like being a graduate student in my lab, but my thesis sucked all the meaning out of my brain and suddenly I can't even manage to put two sentences together that make sense.  So instead, the most useful thing(s) I can leave you all, is (are) my bookmarks!  Those that know me know how incredibly organized (read: obsessive compulsive) I am, so over the last 2.5 years I've collected quite a bit of useful internet knowledge and organized it into various categories on my computer.   So, as my parting gift to you, I leave you these helpful links on everything from job sites, to SAS codes, to data portals, and most importantly, sites for procrastination.  I can't promise these links will stay active forever, but last I checked they worked.  So enjoy!
  1. GIS DATA
  2. From here.
    • FIU GIS Center has some helpful tips/links: http://gis.fiu.edu/maps-data/finding-guides/
    • Everywhere
      • http://datagateway.nrcs.usda.gov/GDGOrder.aspx
      • http://glovis.usgs.gov/
      • http://earthexplorer.usgs.gov/
      • http://data.labins.org/2003/
    • Florida
      • http://www.fgdl.org/metadataexplorer/explorer.jsp
      • http://www.sfwmd.gov/portal/page/portal/levelthree/GIS
      • http://fcelter.fiu.edu/data/GIS/interactive_map/
      • http://sofia.usgs.gov/eden/stationlist-area.php?area=ENP
  3. SAS Codes
  4. From here.
    • A long list of codes: http://core.ecu.edu/psyc/wuenschk/SAS/SAS-Programs.htm
    • Various info on stat methods with SAS examples: http://www.uvm.edu/~dhowell/StatPages/StatHomePage.html
    • Not sure which test to run?  Check this handy dandy table out: http://www.ats.ucla.edu/stat/mult_pkg/whatstat/choosestat.html
    • Poisson: http://www.ats.ucla.edu/stat/sas/dae/poissonreg.htm
    • Repeated Meaures ANOVA: http://www.ats.ucla.edu/stat/sas/library/repeated_ut.htm
    • Linear Models from Littell et al. 2002: http://faculty.ucr.edu/~hanneman/linear_models/c8.html
  5. Job Sites
  6. From here.
    • http://wfscjobs.tamu.edu/job-board/
    • http://fisheries.org/jobs
    • http://www.sws.org/jobs/
    • http://www.erf.org/taxonomy/term/2
    • http://esa.org/careers_certification/jobLists.php
    • http://www.conbio.org/professional-development/scb-job-board/
    • http://www.aslo.org/jobs.html
    • https://careers.nature.org/
    • http://www.nwf.org/About/Jobs-at-NWF.aspx
    • http://www.oceanconservancy.org/who-we-are/about-employment.html
    • http://www.edf.org/jobs
  7. Procrastinate!
  8. From here.
    • http://whatshouldwecallgradschool.tumblr.com/
    • http://www.phdcomics.com/comics.php
    • http://www.mcsweeneys.net/articles/back-from-yet-another-globetrotting-adventure-indiana-jones-checks-his-mail-and-discovers-that-his-bid-for-tenure-has-been-denied
    • http://www.mcsweeneys.net/articles/faq-the-snake-fight-portion-of-your-thesis-defense
    • Cook this cajun dish and thank me later: http://www.nola.com/food/index.ssf/2008/05/lorin_gaudins_crawfish_etouffe.html

Thursday, August 16, 2012

Fish go to school, too

August 16, 2012 0
Greetings from the confines of my office!  I have not posted in over a month but lucky for you, the other bloggers have kept you entertained with Alligator vomit, post-quals stress disorder and the joys of working with carcinogens, flammable materials and high-voltage equipment.  If those don't make you want to be a graduate student and/or scientist, then I don't know what will!

So what have I been doing?  A whole lot of non-exciting blogging material like processing DIDSON videos, analyzing data, and preparing for conferences.  The good news is now I have some results to share!  


One of the most interesting and surprising things I've found in my DIDSON videos is schools of small prey fish (< 12 cm).  Not just one or two on occasion, but nearly every time I go out, in all three of the canals I work in, there are schools.   

Some are small (you may need to make the video full screen to even see them):


Others are quite large:




Some are highly organized and form "bait balls":



Whereas others change shape and direction on a whim:



It's been fascinating to see such a variety of schools.  As far as I know, Everglades' scientists were unaware prey fish were using these canals so prolifically and behaving this way.  Schooling is often times a behavior prey fish employ to avoid being preyed upon by larger fish.  They also school for other reasons (foraging, reproducing), so my next step is to describe, quantitatively, the shape and size of these schools to show this is an anti-predator defense.

Stay tuned!


Tuesday, August 14, 2012

Grad Student Life Beyond Fieldwork: Part 4 (Our Labs)

August 14, 2012 0

Today’s post is the last installment of my series “Grad Student Life Beyond Fieldwork.” Take a look at Part 1 (Classes), Part 2 (Teaching) and Part 3 (Our Offices) to read about other facets of grad student life. Part 4, the post you are reading now, is about the labs where we produce and analyze data.


Some measurements we use for our research, like water temperature and salinity, can be measured directly in the field. Other more complicated things like “cyanobacteria community structure” involve taking field samples back to a lab (or multiple labs) for extensive analysis. Below I have posted a “virtual tour” of the lab I work in, the Microbial Ecology Lab at FIU, to give readers an idea of what grad students and scientists do other than walk around wearing lab coats. 


Above is the door to the lab. It basically says, “Welcome! You are about to encounter biological materials, carcinogens, flammable materials and high voltage equipment! You should probably turn around.” All of these dangers are necessary to understand what microscopic organisms live in water samples from the Everglades and Florida Bay. Although this sign implies that you might die upon opening the door, our lab is generally safe as long as you use common sense and have a little bit of lab safety training. 


Next we enter the lab. Note that just like my office, it has no windows. All scientists are allergic to sunlight.

One line of research conducted in this lab is determining cyanobacteria community structure. While one could look under a microscope at a water drop and take a guess at what kinds of cyanobacteria are in it, genetic techniques have been developed to give a much more accurate picture of what species are in a water sample. Understanding cyanobacteria community structure and factors that impact it is important for Florida Bay water samples because Florida Bay often experiences cyanobacterial blooms. Below is some of the equipment and tools we use to determine community structure.


This is the PCR (polymerase chain reaction) thermocycler, which amplifies segments of cyanobacteria DNA. An extremely small drop of a water sample and several reagents are added to tiny vials then placed in this machine. The machine then repeatedly heats and cools the vials so copies of the desired DNA segment can be made.

How small of a scale are we talking about? Above are the pipets that we use. Notice that they are set in microliters.

Not all laboratory equipment is highly advanced and specialized. While the DNA is synthesized, agarose gels are prepared using the microwave shown above. Since ethidium bromide, a probable carcinogen, is used in the gels, this is not the best place to heat up your lunch. 

After the gel is prepared and solidified, we pipet 5-10 microliters of the amplified DNA into tiny wells in the gel (I am probably really good at the board game “Operation” after doing this hundreds of times). An electric charge is then run across the gel in the gel electrophoresis machine shown above, which moves the DNA down the gel. The distance the DNA travels tells us how long the segment of DNA is. With a few more lab procedures and hours of analysis on Excel, we can determine what species of cyanobacteria were in the original sample.

FCE Grad Students: How much time to you spend in your lab? What are some things you like or don’t like about your lab work?

Other Readers: Do you have any questions or comments about our lab work?  Do you have any questions remaining about grad student life (classes, teaching responsibilities, etc.)?